published_or_final_version / abstract / Biological Sciences / Doctoral / Doctor of Philosophy

published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

This thesis provides an 'immanent' critique of the moral dimension of Hayek's political theory. The concept of morality that Hayek advances is epistemologically founded. That concept is concerned with the recognition and respect of the natural limits of human knowledge and is incompatible with the idea of objective value judgement. The moral dimension of Hayek's theory is based on the methodological implications of his epistemologically founded concept of morality. That dimension consists of the ideas of social spontaneity and cultural evolution and is incompatible with any concept of objective liberal values. The moral dimension of Hayek's theory excludes but also requires substantive politics. The moral exclusion of substantive politics' undermines freedom and equality in catallaxy while, at the same time, it relativises commutative justice and legitimates the minimal state only from the point of view of its legality. Substantive politics is morally required for preserving and promoting institutions such as catallaxy and commutative justice in terms of liberalism. It is argued that the moral exclusion of substantive politics is due to the epistemological premises of Hayek's theory. Those premises form the praxeological presuppositions of social spontaneity and cultural evolution. In terms of them, substantive politics cannot be morally explained. Substantive politics is grounded on a normative/evaluative conception of a social good. That conception depends on critical reason in terms of which objective liberal values can be "recognised and respected. The moral requirement of substantive politics is due to the fact that the process of social spontaneity and cultural evolution cannot by itself be safeguarded against coercion, inequality and injustice.

Tiger salamanders, and especially the Mexican axolotl (Ambystoma mexicanum), are important model organisms in biological research. This dissertation describes new genomic resources and scientific results that greatly extend the utility of tiger salamanders. With respect to new resources, this dissertation describes the development of expressed sequence tags and assembled contigs, a comparative genome map, a web-portal that makes genomic information freely available to the scientific community, and a computer program that compares structure features of organism genomes. With respect to new scientific results, this dissertation describes a quantitative trait locus that is associated with ecologically and evolutionarily relevant variation in developmental timing, the evolutionary history of the tiger salamander genome in relation to other vertebrate genomes, the likely origin of amniote sex chromosomes, and the identification of the Mexican axolotl sex-determining locus. This dissertation is concluded with a brief outline of future research directions that can extend from the works that are presented here.

One of the most intriguing questions in evolutionary biology is how biochemical and structural complexity arise through small and incremental changes; however answering this question requires an explicit set of candidate residues and an experimental system in which to test them. This dissertation aims to understand how biochemical complexity evolves and assesses the structure-function relationship in the green fluorescent protein (GFP) protein family using an ancestral reconstruction approach. In the second chapter, I studied the evolution of biochemical complexity in Kaede-type red fluorescent proteins (FPs) from Faviina corals. An increase in biochemical complexity is represented by the emergence of red fluorescence because it necessitates the synthesis of a tri-cyclic chromophore from a precursor bi-cyclic chromophore through an additional autocatalytic reaction step. The autocatalytic reaction is fully enabled by as many as twelve historical mutations. Here, I showed that the red fluorescent chromophore evolved from an ancestral green chromophore by perturbing the ancestral protein stability at multiple levels of protein structure. Moreover, only three historical mutations are sufficient to initiate the selection-accessible evolutionary trajectory leading to emergence of red fluorescence. The third chapter investigates six mutations proximate to the chromophore in the Kaede-type FP that could have facilitated autocatalytic synthesis of the red chromophore by enlarging the chromophore-containing cavity and modifying its microenvironment. Two of these six mutations were found to strongly affect the protein’s stability and oligomeric tendency. Additionally, I showed that the dimeric least divergent Kaede-type FP, R1-2, evolved from the tetrameric green ancestor. Taken together the results of these studies indicate that the step-up in biochemical complexity in the Kaede-type FPs was achieved via disruption of the existing stable interactions at tertiary and quaternary protein structure levels. In the fourth chapter, I resurrected the common ancestor of all FPs cloned from the order Leptothecata (class Hydrozoa), which are characterized by the highest known homo-oligomeric diversity. I showed that the ancestor was a green monomeric FP with a large Stokes shift. The ancestral FP together with the extant Leptothecata FPs could server as a model system to study the evolution of function and homo-oligomerization, and the desirable photophysical characteristics would make this ancestral FP a useful bio-marker in bio-medical research. / text

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Understanding the maintenance of the variation that is typically observed in natural populations has been a central aim of evolutionary biology. In a feral population of Soay sheep on the island of Hirta, St. Kilda there is a phenotypic polymorphism for horns with males growing either normal or reduced (scurred) horns, and females growing either normal, scurred or no (polled) horns, with further variation in horn size within each of the horn types. This thesis examines the potential factors which maintain these polymorphisms. I first present an overview of the literature relating to the factors that potentially maintain variance in traits in natural populations. In chapter two I present an analysis that suggests that polymorphisms in both horn type and horn size may be maintained by trade-offs between allocation to reproductive success and survival in males, and by sexually antagonistic selection between males and females. In chapter three I test the hypothesis that female weaponry may convey an advantage in intrasexual conflicts over resources, rather than just being expressed as a consequence of genetic associations with the male phenotype. Chapter four examines the environmental factors which create variation between individuals in their horn length, revealing that individuals vary in response to the environment. In chapter five I investigate whether the temporally fluctuating environmental conditions of St. Kilda generate fluctuating selection on the horn length of normal-horned males, revealing that this mechanism constrains the evolution of horn length potentially maintaining variance. In chapter six I examine the genetic relationships between morphological traits, revealing that these relationships are dependent upon the environmental conditions experienced during the first year of life. Finally, I discuss the wider implications of these findings for our understanding of the maintenance of trait variation in the wild.

This thesis investigates the emergence in human evolution of communication through symbols, or conventional, arbitrary signs. Previous work has argued that symbolic speech was preceded by communication through nonarbitrary signs, but how vocal symbolic communication arose out of this has not been extensively studied. Thus far, past research has emphasized the advantages of vocal symbols and pointed to communicative and evolutionary pressures that would have spurred their development. Based on semiotic principles, I examine emergence in terms of two factors underlying symbols: interpretation and conventionalization. I address the question with a consideration of embodied human experience – that is, accounting for the particular features that characterize human communication. This involves simultaneous expression through vocal and gestural modalities, each of which has distinct semiotic properties and serves distinct functions in language today. I examine research on emerging sign systems together with research on properties of human communication to address the question of symbol emergence in terms of the specific context of human evolution. I argue that, instead of in response to pressures for improved communication, symbolic vocalizations could have emerged through blind cultural processes out of the conditions of multimodal nonarbitrary communication in place prior to modern language. Vocalizations would have been interpreted as arbitrary by virtue of their semiotic profile relative to that of gesture, and arbitrary vocalizations could have become conventionalized via the communicative support of nonarbitrary gestures. This scenario avoids appealing to improbable evolutionary and psychological processes and provides a comprehensive and evolutionarily sound explanation for symbol emergence. I present experiments that test hypotheses stemming from this claim. I show that novel arbitrary vocal forms are interpreted and adopted as symbols even when these are uninformative and gesture is the primary mode of communication. I also present computational models that simulate multi-channel, heterosemiotic communication like that of arbitrary speech and nonarbitrary gesture. These demonstrate that information like that provided by gesture can enable the conventionalization of symbols across a population. The results from experiments and simulations together support the claim that symbolic communication could arise naturally from multimodal nonarbitrary communication, offering an explanation for symbol emergence more consistent with evolutionary principles than existing proposals.

First, the literature on hominoid cytogenetics is reviewed and evaluated. It is suggested that there are significant deficiencies in the ways in which chromosomal data have been used with regard to primate evolution. The most robust chromosomal data support an orthodox phylogeny of the Hominoidea. Heterodox phylogenies which have been suggested on the basis of chromosomal data are not well supported. The present investigation considered the problem of intra-specific variation in karyotypes of the common chimpanzee. Blood cultures were cultivated on 25 chimpanzees, constituting the largest sample of chimpanzees in a single cytogenetic study. These were studied by G-banding, C-banding and nucleolar organizer (Ag-NOR) staining. No inversions, translocations, fissions or fusions were detected in this sample. However, several variations of the constitutive heterochromatin and nucleolar organizers were noted. One individual had a chromosome 22 which lacked the heterochromatic short arm and satellite entirely. The most common variants were those in which the amount of telomeric heterochromatin differed significantly between the two homologous chromosomes. One such variant for chromosome 19 was found in 8 individuals. Two of the common chimpanzees possessed a chromosome 23 with a large heterochromatic short arm, although this feature has been reported only for the pygmy chimpanzee. To compare the observable range of variation in the common chimpanzee with its sister group, fibroblast cultures were obtained on three pygmy chimpanzees. Some of the cytotaxonomic distinctions between the two chimpanzee species are called into question. Three main conclusions are drawn from this work. First, the most common kinds of variations are nucleolar organizer and C-band heteromorphisms, as with the chimpanzee's close relative Homo sapiens. Second, inversions and translocations, which seem to be very common among gibbons but not among macaques/baboons, are not common in chimpanzees. This is in accordance with the hypothesis that such structural chromosomal diversity is a property of the social structure of the species rather than a property of the clade to which the species belongs. Third, there is some overlap between Pan paniscus and Pan troglodytes for characters which have been thought to be cytotaxonomically distinctive of each species.

sand hops and bounces -see the dunes grow, run, collide -form the field's pattern.Aeolian sand dune morphologies and sizes are strongly connected to the environmental context and physical processes active since dune formation. As such, the patterns and measurable features found within dunes and dune fields can be interpreted as records of environmental conditions. Using mathematical models of dune and dune field evolution, it should be possible to quantitatively predict dune field dynamics from current conditions or to determine past field conditions based on present-day observations.In this dissertation, we focus on the construction and quantitative analysis of a continuum dune evolution model. We then apply this model towards interpretation of the formative history of terrestrial and martian dunes and dune fields. Our first aim is to identify the controls for the characteristic lengthscales seen in patterned dune fields. Variations in sand flux, binary dune interactions, and topography are evaluated with respect to evolution of individual dunes. Through the use of both quantitative and qualitative multiscale models, these results are then extended to determine the role such processes may play in (de)stabilization of the dune field. We find that sand flux variations and topography generally destabilize dune fields, while dune collisions can yield more similarly-sized dunes. We construct and apply a phenomenological macroscale dune evolution model to then quantitatively demonstrate how dune collisions cause a dune field to evolve into a set of uniformly-sized dunes. Our second goal is to investigate the influence of reversing winds and polar processes in relation to dune slope and morphology. Using numerical experiments, we investigate possible causes of distinctive morphologies seen in Antarctic and martian polar dunes. Finally, we discuss possible model extensions and needed observations that will enable the inclusion of more realistic physical environments in the dune and dune field evolution models.By elucidating the qualitative and quantitative connections between environmental conditions, physical processes, and resultant dune and dune field morphologies, this research furthers our ability to interpret spacecraft images of dune fields, and to use present-day observations to improve our understanding of past terrestrial and martian environments.